Test CMake build process on cerebellum at UCSF

CMakeLists.txt

@@ -85,6 +85,7 @@ set(CMAKE_MODULE_PATH
 #
 # General libraries
 find_package( PkgConfig REQUIRED)
+#pkg_check_modules( metis REQUIRED metis )
 
 
 #
@@ -93,7 +94,7 @@ find_package(DOLFIN REQUIRED CONFIG)
 if(DOLFIN_FOUND)
   message( STATUS "FEniCS found at ${DOLFIN_INCLUDE_DIRS}" )
   include(${DOLFIN_USE_FILE})
-  get_filename_component( DOLFIN_LIBRARY_DIRS ${DOLFIN_LIBRARIES} DIRECTORY )
+  get_filename_component( DOLFIN_LIBRARY_DIRS ${DOLFIN_LIBRARIES} PATH )
 endif()
 
 #
@@ -133,13 +134,23 @@ if(EIGEN_FOUND)
   include_directories(${EIGEN_INCLUDE_DIR})
 endif()
 
+##
+## MPI (FEniCS)
+#find_package(MPI REQUIRED)
+##
+#if( MPI_FOUND )
+#  message(STATUS "MPI found" )# @ ${MPI_INCLUDE_PATH} : ")
+#  include_directories(${MPI_INCLUDE_PATH})
+#endif()
+
+
 #
-# MPI (FEniCS)
-find_package(MPI REQUIRED)
+# Metis
+find_package( METIS REQUIRED )
 #
-if(MPI_FOUND)
-  message(STATUS "MPI found @ ${MPI_INCLUDE_PATH} : ")
-  include_directories(${MPI_INCLUDE_PATH})
+if( METIS_FOUND )
+  message( STATUS "Metis found" )
+  include_directories( ${METIS_INCLUDE_DIR} )
 endif()
 
 #
@@ -156,7 +167,7 @@ endif()
 find_package(CGAL 4.3 REQUIRED)
 #
 if(CGAL_FOUND)
-  message( STATUS "CGAL FOUND ${CGAL_DIR}" )
+  message( STATUS "CGAL found ${CGAL_DIR}" )
   add_definitions( -DCGAL_EIGEN3_ENABLED )
   include( ${CGAL_USE_FILE} )
 endif()

Fijee/Mesh_rendering/Head_conductivity_tensor.h

@@ -43,17 +43,13 @@
 #include "Conductivity_tensor.h"
 #include "CGAL_tools.h"
 #include "Cell_conductivity.h"
-
-#include <metis.h>
 //
 // Eigen
 //
 #include <Eigen/Dense>
 // VTK
 #include <vtkSmartPointer.h>
 #include <vtkMatrix3x3.h>
-//#include <vtkMath.h>
-
 /*! \namespace Domains
  * 
  * Name space for our new package

Fijee/Mesh_rendering/Parcellation_METIS.cxx

@@ -28,8 +28,7 @@
 // 
 // 
 // 
-extern "C"
-{
+extern "C" {
 #include <stdlib.h>     /* calloc, exit, free */
 #include <metis.h>
 }

FijeeConfig.cmake.in

@@ -22,13 +22,15 @@ set( Fijee_INCLUDE_DIRS
   "@EIGEN_INCLUDE_DIR@" 
   "@NIFTI_INCLUDE_DIR@"
   "@CGAL_INCLUDE_DIRS@"
+  "@METIS_INCLUDE_DIR@"
   "@VTK_INCLUDE_DIRS@" 
   "@DOLFIN_INCLUDE_DIRS@" 
   )
 #
 set( Fijee_LIBRARY_DIRS 
   "@Fijee_LIBRARY_DIR@" 
-  "@CGAL_DIR@"
+  "@CGAL_LIBRARIES_DIR@"
+  "@METIS_LIBRARY_DIR@"
   "@VTK_LIBRARY_DIRS@" 
   "@DOLFIN_LIBRARY_DIRS@" 
   )

cmake/modules/FindEIGEN.cmake

@@ -1,12 +1,27 @@
-message(STATUS "Checking for EIGEN3")
+#
+# Find the EIGEN includes and libraries
+#
+# EIGEN is a library that implements a variety of algorithms for
+# linear algebra, sparse matrices. 
+# It can be found at:
+#
+# EIGEN_INCLUDE_DIR - where to find metis.h
+# EIGEN_LIBRARIES   - List of fully qualified libraries to link against.
+# EIGEN_FOUND       - Do not attempt to use if "no" or undefined.
 
+find_path( EIGEN_INCLUDE_DIR Eigen
+  ${EIGEN_DIR}/include/eigen3
+  /usr/include/eigen3
+  /usr/include
+  /opt/local/include
+  /usr/local/include
+  )
 
-if(NOT ${EIGEN_DIR})
-  set(EIGEN_DIR "/usr/include/eigen3")
-endif()
-
-set(EIGEN_INCLUDE_DIR "/usr/include/eigen3")
-
-
-set(EIGEN_FOUND 1)
+if(EIGEN_INCLUDE_DIR)
+  set( EIGEN_FOUND "YES" )
+else()
+  set( EIGEN_FOUND "NO" )
+  message(STATUS "Eigen not found")
+endif( EIGEN_INCLUDE_DIR )
 
+mark_as_advanced( EIGEN_INCLUDE_DIR EIGEN_LIBRARY )

cmake/modules/FindMETIS.cmake

@@ -0,0 +1,37 @@
+#
+# Find the METIS includes and libraries
+#
+# METIS is a library that implements a variety of algorithms for
+# partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of
+# sparse matrices. It can be found at:
+#
+# METIS_INCLUDE_DIR - where to find metis.h
+# METIS_LIBRARIES   - List of fully qualified libraries to link against.
+# METIS_FOUND       - Do not attempt to use if "no" or undefined.
+
+find_path( METIS_INCLUDE_DIR metis.h
+  ${METIS_DIR}/include
+  /opt/local/include
+  /usr/local/include
+  /usr/include
+  /usr/include/metis
+#  $ENV{METIS_DIR}/include
+  )
+
+find_library( METIS_LIBRARY metis
+  HINTS ${METIS_DIR}/lib
+  PATHS /opt/local/lib /usr/local/lib /usr/lib
+#  $ENV{METIS_DIR}/lib
+  )
+#
+get_filename_component( METIS_LIBRARY_DIR "${METIS_LIBRARY}" PATH)
+
+if(METIS_INCLUDE_DIR)
+  add_definitions( -DIDXTYPEWIDTH=64 -DINTSIZE64 )
+
+  if( METIS_LIBRARY )
+    set( METIS_FOUND "YES" )
+  endif( METIS_LIBRARY )
+endif( METIS_INCLUDE_DIR )
+
+mark_as_advanced( METIS_INCLUDE_DIR METIS_LIBRARY )